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Gruneisen fix to follow recent changes of phonopy python interface

This commit is contained in:
Atsushi Togo 2014-02-19 11:39:05 +09:00
parent cc0a4a7b11
commit d81d0fb2f0
4 changed files with 29 additions and 26 deletions
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3
phonopy/__init__.py
View File

@ -395,6 +395,9 @@ class Phonopy:
self._primitive,
self._symprec)
def set_dynamical_matrix(self):
self._set_dynamical_matrix()
def get_dynamical_matrix_at_q(self, q):
self._set_dynamical_matrix()
self._dynamical_matrix.set_dynamical_matrix(q)

2
phonopy/version.py
View File

@ -32,4 +32,4 @@
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
phonopy_version = "1.8.3"
phonopy_version = "1.8.3.1"

38
scripts/gruneisen
View File

@ -54,18 +54,17 @@ def get_phonon(cell_filename,
primitive_axis=np.eye(3),
born_filename=None):
cell = read_vasp(cell_filename)
phonon = Phonopy(cell, dim, is_auto_displacements=False)
phonon.set_force_sets(parse_FORCE_SETS(filename=force_sets_filename))
if born_filename is None:
is_nac = False
else:
is_nac = True
phonon.set_post_process(primitive_axis)
phonon = Phonopy(cell,
dim,
primitive_matrix=primitive_axis,
is_auto_displacements=False)
force_sets = parse_FORCE_SETS(filename=force_sets_filename)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
if born_filename:
phonon.set_nac_params(parse_BORN(phonon.get_primitive(),
filename=born_filename))
nac_params = parse_BORN(phonon.get_primitive(), filename=born_filename)
phonon.set_nac_params(nac_params)
phonon.set_dynamical_matrix()
return phonon
def get_phonon_from_force_constants(cell_filename,
@ -74,17 +73,16 @@ def get_phonon_from_force_constants(cell_filename,
primitive_axis=np.eye(3),
born_filename=None):
cell = read_vasp(cell_filename)
phonon = Phonopy(cell, dim, is_auto_displacements=False)
phonon = Phonopy(cell,
dim,
primitive_matrix=np.eye(3),
is_auto_displacements=False)
force_constants = parse_FORCE_CONSTANTS(force_constants_filename)
is_nac = False
phonon.set_force_constants(force_constants)
if born_filename:
is_nac = True
phonon.set_post_process(primitive_axis,
force_constants=force_constants,
is_nac=is_nac)
if born_filename:
phonon.set_nac_params(parse_BORN(phonon.get_primitive(),
filename=born_filename))
nac_params = parse_BORN(phonon.get_primitive(), filename=born_filename)
phonon.set_nac_params(nac_params)
phonon.set_dynamical_matrix()
return phonon
from optparse import OptionParser

12
setup.py
View File

@ -1,11 +1,13 @@
from distutils.core import setup, Extension
#from setuptools import setup, Extension
import numpy
include_dirs_numpy = [numpy.get_include()]
extension = Extension('phonopy._phonopy',
extra_compile_args=['-fopenmp'],
extra_link_args=['-lgomp'],
# extra_compile_args=['-fopenmp'],
# extra_link_args=['-lgomp'],
include_dirs=['c/harmonic_h'] + include_dirs_numpy,
sources=['c/_phonopy.c',
'c/harmonic/dynmat.c'])
@ -13,8 +15,8 @@ extension = Extension('phonopy._phonopy',
extension_spglib = Extension(
'phonopy._spglib',
include_dirs=['c/spglib_h'] + include_dirs_numpy,
extra_compile_args=['-fopenmp'],
extra_link_args=['-lgomp'],
# extra_compile_args=['-fopenmp'],
# extra_link_args=['-lgomp'],
sources=['c/_spglib.c',
'c/spglib/cell.c',
'c/spglib/debug.c',
@ -36,7 +38,7 @@ extension_spglib = Extension(
setup(name='phonopy',
version='1.8.3',
version='1.8.3.1',
description='This is the phonopy module.',
author='Atsushi Togo',
author_email='atz.togo@gmail.com',